If you want to go with FI, try to find a motor out a newer donor truck that has all of its own wiring with it (ie. computer, harness, sensors, etc.) that way you can just change harnesses. The Jeep 4 cyl. FI harness and computer were made and calibrated for the Jeep 4 cyl. so I doubt that you could, or it would be quite difficult to adapt the Jeep harness and computer to a chevy V8. I dont know if you said you already had an engine lined up, but if not, start checking junkyards and salvage yards for donor trucks. If you want a standard 350ci, look at early to mid 90's 1500's and up trucks. Later they started using the 5.3L engines and i think the blocks arent the same. But if you do want a newer motor, as long as you can get the computer, harness, and sensors, etc. from the donor truck, do it, the engine will have less miles on it and be in better shape generally. you can find adapters to fit the engine to a good tranny you want.
'92 Wrangler, 350ci Chevy w/ Holley Truck Avenger carb, B-W WC T4, NP231 w/ JB conversions SYE, Ford 8.8 rearend w/ ARB, Dana 44 front w/ ARB, 4.10's, Rubicon Express XD 4.5" lift, 35" MT/R's on 15"x8" American Racing wheels, 6" Bushwacker cut-out TJ-style fender flares, custom polished aluminum dash w/ full set of Autometer Ultra-Lite gauges, Warn HS9500i winch, Big Daddy Step Rock Rails, custom, self-made rear bumper